From unknown Mon Aug 18 06:58:11 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#71339] [PATCH] gnu: Add r-scent. Resent-From: "Afkhami, Navid" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 03 Jun 2024 14:22:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 71339 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 71339@debbugs.gnu.org Cc: "Afkhami, Navid" X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.171742451521362 (code B ref -1); Mon, 03 Jun 2024 14:22:01 +0000 Received: (at submit) by debbugs.gnu.org; 3 Jun 2024 14:21:55 +0000 Received: from localhost ([127.0.0.1]:42149 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sE8ZO-0005YS-MY for submit@debbugs.gnu.org; Mon, 03 Jun 2024 10:21:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:35232) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sE8ZJ-0005YF-Ec for submit@debbugs.gnu.org; Mon, 03 Jun 2024 10:21:52 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sE8Z6-0003AO-0E for guix-patches@gnu.org; Mon, 03 Jun 2024 10:21:36 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sE8Z3-0002xX-La for guix-patches@gnu.org; Mon, 03 Jun 2024 10:21:35 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1717424474; x=1719238875; bh=gchvpcMCybicKX9 HGJMnKuSQ9Q33hSOLjavO9MEb6b8=; b=p5qmhwF74KxhPn2pOgEwyOs5RMJX3Im qjlBL8Kl8ldXJ+Pj4P4+DkUukMhfBGdKAkmfQLqaZFslZvsu0YWWzXpkEL/Xijf+ HcdpfmGIqwLwJKt6mhOfq2di7ct/COslAYFBCA7KNGQvdTCQ8+LqdjFJxAWWm3yH pEwE0OWdNxV0= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8D11E160146 for ; Mon, 3 Jun 2024 16:21:14 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1544.11; Mon, 3 Jun 2024 16:21:14 +0200 From: "Afkhami, Navid" Date: Mon, 3 Jun 2024 14:19:55 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.2019-28430.000 X-TM-AS-Result: No-10--5.743100-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2tYhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUXJ5suMuDH9GX7N8/O92sJRFj276yv/MdYBS4BO08ckNf0iqNWpSwuD4mDuxB3Odot0l 6Beef2vJmrvwYaOdtcchIRNsxA4ZmAl2KRt2ytpKwHXnHVkAsxb2XNUZZqZaA4ftEeSASkbK/2t J3foSBQtCgcFayVUiIB73xunbyKroik8BQ/TD68uhy4rv4kGUkABclkxOrxD9c1aMcEqF1vYuKK HTbs44c23VBUy18Y7rIWq6FUoB6/A== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.743100-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28430.000 X-TM-SNTS-SMTP: 49839BCF8EB2260F889D9FE481FF631DDFFA7FD69D92DA22B8375085E17840472000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioinformatics.scm (r-scent): New variable. Change-Id: Ie517c0619683590f630013982e831fad528c1dea --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cecd94bbb7..cdda029809 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1171,6 +1171,43 @@ (define-public r-scenic ;; GPLv3. (license license:gpl3)))) +(define-public r-scent + (let ((commit "f01f18ac30f8a9bcf85b738c6c7815017e2c8ee5") + (revision "1")) + (package + (name "r-scent") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/immunogenomics/SCENT") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "18krksy8ac7yy8hghzaxscj91c61j195yg7j60zswdq97islvfzi")))) + (properties `((upstream-name . "SCENT"))) + (build-system r-build-system) + (inputs (list bedtools)) + (propagated-inputs (list r-boot + r-data-table + r-hmisc + r-lme4 + r-mass + r-matrix + r-r-utils + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/immunogenomics/SCENT") + (synopsis + "Single-Cell enhancer target gene mapping for multimodal single-cell data") + (description + "This package contains functions for the SCENT algorithm. +SCENT uses single-cell multimodal data and links ATAC-seq peaks +to their target genes by modeling association between chromatin +accessibility and gene expression across individual single cells.") + (license license:expat)))) + (define-public r-saige (let ((commit "c6717ba9c5a967bcf612e97566d845397b1b7167") (revision "1")) base-commit: 1615084a9a4115d48b75b3db048761e7534efc87 -- 2.34.1 From unknown Mon Aug 18 06:58:11 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: "Afkhami, Navid" Subject: bug#71339: closed ([PATCH] gnu: Add r-scent.) Message-ID: References: <87y172zp5l.fsf@elephly.net> X-Gnu-PR-Message: they-closed 71339 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 71339@debbugs.gnu.org Date: Tue, 18 Jun 2024 07:28:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1718695682-29056-1" This is a multi-part message in MIME format... ------------=_1718695682-29056-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #71339: [PATCH] gnu: Add r-scent. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 71339@debbugs.gnu.org. --=20 71339: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D71339 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1718695682-29056-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 71339-done) by debbugs.gnu.org; 18 Jun 2024 07:27:49 +0000 Received: from localhost ([127.0.0.1]:41242 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sJTFt-0007YD-Ey for submit@debbugs.gnu.org; Tue, 18 Jun 2024 03:27:49 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21143) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sJTFr-0007Y4-0x for 71339-done@debbugs.gnu.org; Tue, 18 Jun 2024 03:27:48 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1718695660; cv=none; d=zohomail.com; s=zohoarc; b=Nb3tSWPtSXOfAeIyqcKxyuiFdn78xJAMJ6krCkVjA6EZ6jZR6McDqcStpEYQbpnF00iVIKcQ+q5arEsXO0M/sYWCHI15bf5ScX+hZrxU5jpMhBwilqjVZ4b5zg0VHZtE4ArwulMl5438q8oct4kNbCuC/ntCLh+nvyFzfSI7pXk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1718695660; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=Mpm2rfamMpeLkdv8wHv52RJaCDt7rEr5uLxmhHlq4gE=; b=U5m+HqdXQzT7ntRCbMB0NcMdiil24BRk2pVnTJaav4CskPh2wR5OoupXIz+UQKOIuqrfN+2PQoQfgWBaMUIo3ytv/gDX2tdkqFWp/4oj5DyH3OkJZYlSdFHEg8fmdTiUJ+M3dVbyT9bdrRzYajaTCPhEEc/vQaPDdtpeT8TEvGI= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1718695660; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=Mpm2rfamMpeLkdv8wHv52RJaCDt7rEr5uLxmhHlq4gE=; b=WUdHgF9xKSG+UK4E0mjKXozpJi9LapnKrE1R1ajumV2eV3QC+NLXmFZUIZOAGDbO bN3dJ14jZfJMrwTezooXdWSkyAsazC+NNo2tFxfRFp5m3TYNREhd7FCbLVffXXEm+HH /RuEw18ACQVpV+ot70oeSa2FMZ2x0lwrOduEeYqc= Received: by mx.zohomail.com with SMTPS id 1718695657735130.8020058693039; Tue, 18 Jun 2024 00:27:37 -0700 (PDT) From: Ricardo Wurmus To: 71339-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-scent. Date: Tue, 18 Jun 2024 09:27:34 +0200 Message-ID: <87y172zp5l.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 71339-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Thanks for the patch. Applied! -- Ricardo ------------=_1718695682-29056-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 Jun 2024 14:21:55 +0000 Received: from localhost ([127.0.0.1]:42149 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sE8ZO-0005YS-MY for submit@debbugs.gnu.org; Mon, 03 Jun 2024 10:21:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:35232) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sE8ZJ-0005YF-Ec for submit@debbugs.gnu.org; Mon, 03 Jun 2024 10:21:52 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sE8Z6-0003AO-0E for guix-patches@gnu.org; Mon, 03 Jun 2024 10:21:36 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sE8Z3-0002xX-La for guix-patches@gnu.org; Mon, 03 Jun 2024 10:21:35 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1717424474; x=1719238875; bh=gchvpcMCybicKX9 HGJMnKuSQ9Q33hSOLjavO9MEb6b8=; b=p5qmhwF74KxhPn2pOgEwyOs5RMJX3Im qjlBL8Kl8ldXJ+Pj4P4+DkUukMhfBGdKAkmfQLqaZFslZvsu0YWWzXpkEL/Xijf+ HcdpfmGIqwLwJKt6mhOfq2di7ct/COslAYFBCA7KNGQvdTCQ8+LqdjFJxAWWm3yH pEwE0OWdNxV0= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8D11E160146 for ; Mon, 3 Jun 2024 16:21:14 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1544.11; Mon, 3 Jun 2024 16:21:14 +0200 From: "Afkhami, Navid" To: Subject: [PATCH] gnu: Add r-scent. Date: Mon, 3 Jun 2024 14:19:55 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.2019-28430.000 X-TM-AS-Result: No-10--5.743100-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2tYhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUXJ5suMuDH9GX7N8/O92sJRFj276yv/MdYBS4BO08ckNf0iqNWpSwuD4mDuxB3Odot0l 6Beef2vJmrvwYaOdtcchIRNsxA4ZmAl2KRt2ytpKwHXnHVkAsxb2XNUZZqZaA4ftEeSASkbK/2t J3foSBQtCgcFayVUiIB73xunbyKroik8BQ/TD68uhy4rv4kGUkABclkxOrxD9c1aMcEqF1vYuKK HTbs44c23VBUy18Y7rIWq6FUoB6/A== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.743100-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28430.000 X-TM-SNTS-SMTP: 49839BCF8EB2260F889D9FE481FF631DDFFA7FD69D92DA22B8375085E17840472000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: "Afkhami, Navid" X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioinformatics.scm (r-scent): New variable. Change-Id: Ie517c0619683590f630013982e831fad528c1dea --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cecd94bbb7..cdda029809 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1171,6 +1171,43 @@ (define-public r-scenic ;; GPLv3. (license license:gpl3)))) +(define-public r-scent + (let ((commit "f01f18ac30f8a9bcf85b738c6c7815017e2c8ee5") + (revision "1")) + (package + (name "r-scent") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/immunogenomics/SCENT") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "18krksy8ac7yy8hghzaxscj91c61j195yg7j60zswdq97islvfzi")))) + (properties `((upstream-name . "SCENT"))) + (build-system r-build-system) + (inputs (list bedtools)) + (propagated-inputs (list r-boot + r-data-table + r-hmisc + r-lme4 + r-mass + r-matrix + r-r-utils + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/immunogenomics/SCENT") + (synopsis + "Single-Cell enhancer target gene mapping for multimodal single-cell data") + (description + "This package contains functions for the SCENT algorithm. +SCENT uses single-cell multimodal data and links ATAC-seq peaks +to their target genes by modeling association between chromatin +accessibility and gene expression across individual single cells.") + (license license:expat)))) + (define-public r-saige (let ((commit "c6717ba9c5a967bcf612e97566d845397b1b7167") (revision "1")) base-commit: 1615084a9a4115d48b75b3db048761e7534efc87 -- 2.34.1 ------------=_1718695682-29056-1--